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Old 07-08-2008, 07:38 PM   #38
Senior Member
Location: Kuala Lumpur, Malaysia

Join Date: Mar 2008
Posts: 126
Default Fast Short Read Aligner

First official release of novoalign & novopaired are now available for download at Alignment with qualities and gaps for single end and paired end reads. small RNA mode, adapter stripping, trimming etc.
Can set number of mismatches from 0 to 8 (8 is only suitable on small genomes).
1M CElegans reads in 96s at ++2mismatches*
1M HSapiens reads in 32m at ++2mismatches*
*maybe more than two mismatches as result of quality based scoring
*single threaded 2.4Ghz CPU, 8Gb RAM
Free for non-commercial/open projects.

Last edited by sparks; 07-09-2008 at 08:15 PM.
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